I am Android, so I sometimes have a problem in this area, but clearly that's not Passbook related. It's one reason I try to print PDFs out as well as the App. It's probably just a temporary glitch. Personally I would use your PDF, it may get rejected at T5 conformance, so allow a few minutes to go to Visa Check if necessary, but then have a discussion in the lounge. Does PC MMB still have you in your original seat?
There are some airports that still don't accept the App, but do allow PYOBP. TFS is in that category, ALC I think allows neither.